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- PDB-1t1n: CRYSTAL STRUCTURE OF CARBONMONOXY HEMOGLOBIN -

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Basic information

Entry
Database: PDB / ID: 1t1n
TitleCRYSTAL STRUCTURE OF CARBONMONOXY HEMOGLOBIN
Components(PROTEIN (HEMOGLOBIN)) x 2
KeywordsOXYGEN TRANSPORT / HEMOGLOBIN
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen carrier activity / hydrogen peroxide catabolic process / peroxidase activity / oxygen binding / blood microparticle / iron ion binding ...haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen carrier activity / hydrogen peroxide catabolic process / peroxidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha-1 / Hemoglobin subunit beta-1/2
Similarity search - Component
Biological speciesTrematomus newnesi (dusky notothen)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMazzarella, L. / Vitagliano, L. / Savino, C. / Zagari, A.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of Trematomus newnesi haemoglobin re-opens the root effect question.
Authors: Mazzarella, L. / D'Avino, R. / di Prisco, G. / Savino, C. / Vitagliano, L. / Moody, P.C.E. / Zagari, A.
History
DepositionMar 5, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 29, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 11, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (HEMOGLOBIN)
B: PROTEIN (HEMOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2396
Polymers31,9502
Non-polymers1,2894
Water91951
1
A: PROTEIN (HEMOGLOBIN)
B: PROTEIN (HEMOGLOBIN)
hetero molecules

A: PROTEIN (HEMOGLOBIN)
B: PROTEIN (HEMOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,47712
Polymers63,8994
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12850 Å2
ΔGint-112 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.170, 88.060, 55.250
Angle α, β, γ (deg.)90.00, 97.65, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein PROTEIN (HEMOGLOBIN) / HBTNCO


Mass: 15703.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HEM GROUP IS COMPLEXED WITH CARBON MONOXIDE / Source: (natural) Trematomus newnesi (dusky notothen) / Cell: RED BLOOD CELLS / Tissue: BLOOD / References: UniProt: P45718
#2: Protein PROTEIN (HEMOGLOBIN) / HBTNCO


Mass: 16246.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HEM GROUP IS COMPLEXED WITH CARBON MONOXIDE / Source: (natural) Trematomus newnesi (dusky notothen) / Cell: RED BLOOD CELLS / Tissue: BLOOD / References: UniProt: P45720
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 64 %
Crystal growpH: 8 / Details: pH 8.0
Components of the solutions
IDNameCrystal-IDSol-ID
1tris11
2(NH4)2SO411
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1
250 mMTris-HCl1
32.0 Mammonium sulfate12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 15, 1993 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 25207 / % possible obs: 99.5 % / Redundancy: 2.5 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.3
Reflection shellResolution: 2.1→2.2 Å / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 68936

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
MOSFLMdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PBX

1pbx


Resolution: 2.2→16 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflection
Rwork0.192 --
obs-18129 82.4 %
Displacement parametersBiso mean: 37 Å2
Refinement stepCycle: LAST / Resolution: 2.2→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 90 51 2388
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.364
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.79
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.572
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.861.4
X-RAY DIFFRACTIONx_mcangle_it1.511.4
X-RAY DIFFRACTIONx_scbond_it1.52
X-RAY DIFFRACTIONx_scangle_it2.372
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.79
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.572

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